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commit/galaxy-central: dannon: Remove ftype from mosaik/freebayes test outputs.
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c44bf3bfdec5/ changeset: r5152:c44bf3bfdec5 user: dannon date: 2011-03-02 14:38:19 summary: Remove ftype from mosaik/freebayes test outputs. affected #: 2 files (24 bytes) --- a/tools/human_genome_variation/freebayes.xml Wed Mar 02 08:28:30 2011 -0500 +++ b/tools/human_genome_variation/freebayes.xml Wed Mar 02 08:38:19 2011 -0500 @@ -115,7 +115,7 @@ <param name="reference" ftype="fasta" value="mosaik_test_ref.fasta"/><param name="bamfile" ftype="bam" value="freebayes_in.bam"/><param name="source_select" value="pre_set"/> - <output name="output" ftype="vcf" file="freebayes_out.vcf" lines_diff="4"/> + <output name="output" file="freebayes_out.vcf" lines_diff="4"/></test></tests><help> --- a/tools/sr_mapping/mosaik.xml Wed Mar 02 08:28:30 2011 -0500 +++ b/tools/sr_mapping/mosaik.xml Wed Mar 02 08:38:19 2011 -0500 @@ -94,7 +94,7 @@ <param name="act" value="35"/><param name="bw" value="19"/><param name="mhp" value="100"/> - <output name="output" ftype="sam" file="mosaik_test_out.sam" compare="sim_size" delta="0"/> + <output name="output" file="mosaik_test_out.sam" compare="sim_size" delta="0"/></test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Drop the ftype attribute from tophat test outputs
by Bitbucket 02 Mar '11

02 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0d30654210e9/ changeset: r5151:0d30654210e9 user: natefoo date: 2011-03-02 14:28:30 summary: Drop the ftype attribute from tophat test outputs affected #: 1 file (118 bytes) --- a/tools/ngs_rna/tophat_wrapper.xml Tue Mar 01 16:39:46 2011 -0500 +++ b/tools/ngs_rna/tophat_wrapper.xml Wed Mar 02 08:28:30 2011 -0500 @@ -412,8 +412,8 @@ <param name="sPaired" value="single" /><param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" /><param name="sSettingsType" value="preSet" /> - <output name="junctions" file="tophat_out1j.bed" ftype="bed" /> - <output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" ftype="bam" /> + <output name="junctions" file="tophat_out1j.bed" /> + <output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" /></test><test> @@ -428,8 +428,8 @@ <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" /><param name="mate_inner_distance" value="20" /><param name="pSettingsType" value="preSet" /> - <output name="junctions" file="tophat_out2j.bed" ftype="bed" /> - <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" ftype="bam" /> + <output name="junctions" file="tophat_out2j.bed" /> + <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" /></test><test> @@ -469,10 +469,10 @@ <param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" /><param name="microexon_search" value="Yes" /> - <output name="insertions" file="tophat_out3i.bed" ftype="bed"/> - <output name="deletions" file="tophat_out3d.bed" ftype="bed"/> - <output name="junctions" file="tophat_out3j.bed" ftype="bed" /> - <output name="accepted_hits" file="tophat_out3h.bam" compare="sim_size" ftype="bam" /> + <output name="insertions" file="tophat_out3i.bed" /> + <output name="deletions" file="tophat_out3d.bed" /> + <output name="junctions" file="tophat_out3j.bed" /> + <output name="accepted_hits" file="tophat_out3h.bam" compare="sim_size" /></test><test> @@ -512,8 +512,8 @@ <param name="min_coverage_intron" value="50" /><param name="max_coverage_intron" value="20000" /><param name="microexon_search" value="Yes" /> - <output name="junctions" file="tophat_out4j.bed" ftype="bed" /> - <output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" ftype="bam" /> + <output name="junctions" file="tophat_out4j.bed" /> + <output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" /></test></tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: trackster: Difference view setting for ReadTracks: only see sequence on reads if they don't match reference. Align sequence with positional ticks.
by Bitbucket 01 Mar '11

01 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/24028b35c1cc/ changeset: r5150:24028b35c1cc user: kanwei date: 2011-03-01 22:39:46 summary: trackster: Difference view setting for ReadTracks: only see sequence on reads if they don't match reference. Align sequence with positional ticks. affected #: 1 file (1.1 KB) --- a/static/scripts/trackster.js Tue Mar 01 15:46:35 2011 -0500 +++ b/static/scripts/trackster.js Tue Mar 01 16:39:46 2011 -0500 @@ -9,15 +9,16 @@ * rectangles instead. */ CanvasRenderingContext2D.prototype.dashedLine = function(x1, y1, x2, y2, dashLen) { - if (dashLen == undefined) { dashLen = 4; } + if (dashLen === undefined) { dashLen = 4; } var dX = x2 - x1; var dY = y2 - y1; var dashes = Math.floor(Math.sqrt(dX * dX + dY * dY) / dashLen); var dashX = dX / dashes; var dashY = dY / dashes; + var q; - for (var q= 0; q < dashes; q++, x1 += dashX, y1 += dashY) { - if (q % 2 != 0) { + for (q = 0; q < dashes; q++, x1 += dashX, y1 += dashY) { + if (q % 2 !== 0) { continue; } this.fillRect(x1, y1, dashLen, 1); @@ -45,7 +46,7 @@ this.fill(); this.stroke(); this.closePath(); -} +}; /** * Make `element` sortable in parent by dragging `handle` (a selector) @@ -54,8 +55,9 @@ element.bind( "drag", { handle: handle, relative: true }, function ( e, d ) { var parent = $(this).parent(); var children = parent.children(); + var i; // Determine new position - for ( var i = 0; i < children.length; i++ ) { + for ( i = 0; i < children.length; i++ ) { if ( d.offsetY < $(children.get(i)).position().top ) { break; } @@ -63,12 +65,12 @@ // If not already in the right place, move. Need // to handle the end specially since we don't have // insert at index - if ( i == children.length ) { - if ( this != children.get( i - 1 ) ) { + if ( i === children.length ) { + if ( this !== children.get( i - 1 ) ) { parent.append( this ); } } - else if ( this != children.get( i ) ) { + else if ( this !== children.get( i ) ) { $(this).insertBefore( children.get( i ) ); } }); @@ -115,7 +117,7 @@ * Returns true if there is any overlap between regions. */ function is_overlap(first_region, second_region) { - return (compute_overlap(first_region, second_region) != NO_OVERLAP); + return (compute_overlap(first_region, second_region) !== NO_OVERLAP); } /** @@ -129,7 +131,8 @@ NO_DETAIL_TRACK_HEIGHT = 3, SQUISH_TRACK_HEIGHT = 5, PACK_TRACK_HEIGHT = 10, - NO_DETAIL_FEATURE_HEIGHT = DENSE_FEATURE_HEIGHT = 1, + NO_DETAIL_FEATURE_HEIGHT = 1, + DENSE_FEATURE_HEIGHT = 1, SQUISH_FEATURE_HEIGHT = 3, PACK_FEATURE_HEIGHT = 9, LABEL_SPACING = 2, @@ -206,7 +209,7 @@ $.extend(Cache.prototype, { get: function(key) { var index = this.key_ary.indexOf(key); - if (index != -1) { + if (index !== -1) { this.move_key_to_end(key, index); } return this.obj_cache[key]; @@ -558,11 +561,11 @@ // // If user is navigating to previous/next set of chroms, load new chrom set and return. // - if (chrom == "previous") { + if (chrom === "previous") { view.load_chroms({low: this.chrom_start_index - MAX_CHROMS_SELECTABLE}); return; } - if (chrom == "next") { + if (chrom === "next") { view.load_chroms({low: this.chrom_start_index + MAX_CHROMS_SELECTABLE}); return; } @@ -797,7 +800,7 @@ // Uses a dictionary to construct a tool object. var get_tool_from_dict = function(tool_dict) { - if (obj_length(tool_dict) == 0) { + if (obj_length(tool_dict) === 0) { return undefined; } @@ -901,7 +904,7 @@ for (var i = 0; i < filters_dict.length; i++) { var filter_dict = filters_dict[i]; var name = filter_dict.name, type = filter_dict.type, index = filter_dict.index; - if (type == 'int' || type == 'float') { + if (type === 'int' || type === 'float') { filters[i] = new NumberFilter(name, index); } else { filters[i] = new Filter(name, index, type); @@ -938,9 +941,9 @@ var id = 'param_' + index; var row = $("<div class='form-row' />").appendTo( container ); row.append( $('<label />').attr("for", id ).text( param.label + ":" ) ); - if ( param.type == 'bool' ) { + if ( param.type === 'bool' ) { row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', track_config.values[ param.key ] ) ); - } else if ( param.type == 'color' ) { + } else if ( param.type === 'color' ) { var value = track_config.values[ param.key ]; var input = $('<input />').attr("id", id ).attr("name", id ).val( value ); // Color picker in tool tip style float @@ -978,11 +981,11 @@ // Parse value from form element var id = 'param_' + index; var value = container.find( '#' + id ).val(); - if ( param.type == 'float' ) { + if ( param.type === 'float' ) { value = parseFloat( value ); - } else if ( param.type == 'int' ) { + } else if ( param.type === 'int' ) { value = parseInt( value ); - } else if ( param.type == 'bool' ) { + } else if ( param.type === 'bool' ) { value = container.find( '#' + id ).is( ':checked' ); } // Save value only if changed @@ -1066,7 +1069,7 @@ return; } - if ( track.view.chrom != null ) { + if ( track.view.chrom !== null ) { // Get dataset state; if state is fine, enable and draw track. Otherwise, show message // about track status. $.getJSON(converted_datasets_state_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, chrom: track.view.chrom}, @@ -1636,7 +1639,7 @@ new_track; // TODO: add support for other kinds of tool data tracks. - if (current_track.track_type == 'FeatureTrack') { + if (current_track.track_type === 'FeatureTrack') { new_track = new ToolDataFeatureTrack(track_name, view, undefined, {}, {}, current_track); } @@ -1647,7 +1650,7 @@ // Run tool. var json_run_tool = function() { $.getJSON(run_tool_url, url_params, function(track_data) { - if (track_data == "no converter") { + if (track_data === "no converter") { // No converter available for input datasets, so cannot run tool. new_track.container_div.addClass("error"); new_track.content_div.text(DATA_NOCONVERTER); @@ -1657,7 +1660,7 @@ new_track.container_div.addClass("error"); new_track.content_div.text(DATA_CANNOT_RUN_TOOL + track_data.message); } - else if (track_data == "pending") { + else if (track_data === "pending") { // Converting/indexing input datasets; show message and try again. new_track.container_div.addClass("pending"); new_track.content_div.text("Converting input data so that it can be easily reused."); @@ -1739,8 +1742,10 @@ Track.call( this, null, view, view.top_labeltrack ); TiledTrack.call( this ); + view.reference_track = this; this.left_offset = 200; this.height_px = 12; + this.font = DEFAULT_FONT; this.container_div.addClass( "reference-track" ); this.content_div.css("background", "none"); this.content_div.css("min-height", "0px"); @@ -1750,19 +1755,21 @@ this.tile_cache = new Cache(CACHED_TILES_LINE); }; $.extend( ReferenceTrack.prototype, TiledTrack.prototype, { - get_data: function(resolution, position) { + get_data: function(resolution, tile_index, key) { var track = this, - low = position * DENSITY * resolution, - high = ( position + 1 ) * DENSITY * resolution, - key = resolution + "_" + position; - - if (!track.data_queue[key]) { - track.data_queue[key] = true; + low = tile_index * DENSITY * resolution, + high = ( tile_index + 1 ) * DENSITY * resolution, + internal_key = low + "_" + high; + + if (key === undefined) { key = internal_key; } + if (!track.data_queue[internal_key]) { + track.data_queue[internal_key] = true; $.ajax({ 'url': reference_url, 'dataType': 'json', 'data': { "chrom": this.view.chrom, "low": low, "high": high, "dbkey": this.view.dbkey }, success: function (seq) { track.data_cache.set(key, seq); - delete track.data_queue[key]; + track.data_cache.set(internal_key, seq); + delete track.data_queue[internal_key]; track.draw(); }, error: function(r, t, e) { console.log(r, t, e); @@ -1770,6 +1777,12 @@ }); } }, + range_data: function(low, high) { + var key = low + "_" + high; + + var data = this.data_cache.get(key); + return data; + }, draw_tile: function( resolution, tile_index, parent_element, w_scale ) { var tile_low = tile_index * DENSITY * resolution, tile_length = DENSITY * resolution, @@ -1783,7 +1796,7 @@ if (w_scale > CHAR_WIDTH_PX) { if (this.data_cache.get(key) === undefined) { - this.get_data( resolution, tile_index ); + this.get_data(resolution, tile_index, key); return; } @@ -1795,11 +1808,12 @@ canvas.get(0).width = Math.ceil( tile_length * w_scale + this.left_offset); canvas.get(0).height = this.height_px; - + ctx.font = DEFAULT_FONT; + ctx.textAlign = "center"; for (var c = 0, str_len = seq.length; c < str_len; c++) { - var c_start = Math.round(c * w_scale), - gap = Math.round(w_scale / 2); - ctx.fillText(seq[c], c_start + this.left_offset + gap, 10); + var c_start = Math.round(c * w_scale); + + ctx.fillText(seq[c], c_start + this.left_offset, 10); } parent_element.append(canvas); return canvas; @@ -2225,7 +2239,7 @@ // if slot can be found. // TODO: are there any checks we need to do to ensure that text // will fit on tile? - if (text_align == "left") { + if (text_align === "left") { f_start -= text_len; f_end -= text_len; text_align = "right"; @@ -2346,11 +2360,11 @@ // Set vars that depend on mode. var thin_height, thick_height; - if (mode == "Squish") { + if (mode === "Squish") { thin_height = 1; thick_height = SQUISH_FEATURE_HEIGHT; } - else { // mode == "Pack" + else { // mode === "Pack" thin_height = 5; thick_height = PACK_FEATURE_HEIGHT; } @@ -2359,9 +2373,9 @@ if (!feature_blocks) { // If there are no blocks, treat the feature as one big exon. if ( feature.strand ) { - if (feature.strand == "+") { + if (feature.strand === "+") { ctx.fillStyle = RIGHT_STRAND_INV; - } else if (feature.strand == "-") { + } else if (feature.strand === "-") { ctx.fillStyle = LEFT_STRAND_INV; } } @@ -2381,18 +2395,18 @@ // Draw whole feature as connector/intron. var cur_y_center, cur_height; - if (mode == "Squish") { + if (mode === "Squish") { ctx.fillStyle = CONNECTOR_COLOR; cur_y_center = y_center + Math.floor(SQUISH_FEATURE_HEIGHT/2) + 1; cur_height = 1; } - else { // mode == "Pack" + else { // mode === "Pack" if (feature_strand) { var cur_y_center = y_center; var cur_height = thick_height; - if (feature_strand == "+") { + if (feature_strand === "+") { ctx.fillStyle = RIGHT_STRAND; - } else if (feature_strand == "-") { + } else if (feature_strand === "-") { ctx.fillStyle = LEFT_STRAND; } } @@ -2546,7 +2560,7 @@ // canvas.get(0).width = width + left_offset; canvas.get(0).height = required_height; - if (result.dataset_type == "summary_tree") { + if (result.dataset_type === "summary_tree") { // Increase canvas height in order to display max label. canvas.get(0).height += LABEL_SPACING + CHAR_HEIGHT_PX; } @@ -2697,6 +2711,7 @@ var ReadTrack = function (name, view, hda_ldda, dataset_id, prefs, filters) { FeatureTrack.call(this, name, view, hda_ldda, dataset_id, prefs, filters); this.track_type = "ReadTrack"; + this.difference_mode = true; }; $.extend(ReadTrack.prototype, TiledTrack.prototype, FeatureTrack.prototype, { /** @@ -2704,17 +2719,22 @@ */ draw_read: function(ctx, mode, w_scale, tile_low, tile_high, feature_start, cigar, orig_seq, y_center) { ctx.textAlign = "center"; - var - tile_region = [tile_low, tile_high], - base_offset = 0, + var tile_region = [tile_low, tile_high], + base_offset = 0, seq_offset = 0, - gap = Math.round(w_scale / 2); + gap = 0, + seq_data; // Keep list of triangles that need to be drawn on top of initial drawing layer. // TODO: Eventually, we'll probably want to keep an ordered list of items to draw and then draw all // items at once. var draw_last = []; - + if (view.reference_track) { + seq_data = view.reference_track.range_data(tile_low, tile_high); + } + if ((mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) { + gap = Math.round(w_scale/2); + } for (var cig_id = 0, len = cigar.length; cig_id < len; cig_id++) { var cig = cigar[cig_id], cig_op = "MIDNSHP=X"[cig[0]], @@ -2737,28 +2757,31 @@ case "M": // Match. case "=": // Equals. var seq_tile_overlap = compute_overlap([seq_start, seq_start + cig_len], tile_region); - if (seq_tile_overlap != NO_OVERLAP) { + if (seq_tile_overlap !== NO_OVERLAP) { // Draw. var seq = orig_seq.slice(seq_offset, seq_offset + cig_len); - if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) { + if (gap > 0) { ctx.fillStyle = this.prefs.block_color; - ctx.fillRect(s_start + this.left_offset, y_center + 1, s_end - s_start, 9); + ctx.fillRect(s_start + this.left_offset - gap, y_center + 1, s_end - s_start, 9); ctx.fillStyle = CONNECTOR_COLOR; // TODO: this can be made much more efficient by computing the complete sequence // to draw and then drawing it. for (var c = 0, str_len = seq.length; c < str_len; c++) { + if (this.difference_mode && seq_data && seq_data[seq_start - tile_low + c] === seq[c]) { + continue; + } if (seq_start + c >= tile_low && seq_start + c <= tile_high) { var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); - ctx.fillText(seq[c], c_start + this.left_offset + gap, y_center + 9); + ctx.fillText(seq[c], c_start + this.left_offset, y_center + 9); } } } else { ctx.fillStyle = this.prefs.block_color; // TODO: This is a pretty hack-ish way to fill rectangle based on mode. ctx.fillRect(s_start + this.left_offset, - y_center + (this.mode != "Dense" ? 4 : 5), + y_center + (this.mode !== "Dense" ? 4 : 5), s_end - s_start, - (mode != "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT) ); + (mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT) ); } } seq_offset += cig_len; @@ -2766,14 +2789,14 @@ break; case "N": // Skipped bases. ctx.fillStyle = CONNECTOR_COLOR; - ctx.fillRect(s_start + this.left_offset, y_center + 5, s_end - s_start, 1); + ctx.fillRect(s_start + this.left_offset - gap, y_center + 5, s_end - s_start, 1); //ctx.dashedLine(s_start + this.left_offset, y_center + 5, this.left_offset + s_end, y_center + 5); // No change in seq_offset because sequence not used when skipping. base_offset += cig_len; break; case "D": // Deletion. ctx.fillStyle = "red"; - ctx.fillRect(s_start + this.left_offset, y_center + 4, s_end - s_start, 3); + ctx.fillRect(s_start + this.left_offset - gap, y_center + 4, s_end - s_start, 3); // TODO: is this true? No change in seq_offset because sequence not used when skipping. base_offset += cig_len; break; @@ -2788,7 +2811,7 @@ // Check to see if sequence should be drawn at all by looking at the overlap between // the sequence region and the tile region. var seq_tile_overlap = compute_overlap([seq_start, seq_start + cig_len], tile_region); - if (seq_tile_overlap != NO_OVERLAP) { + if (seq_tile_overlap !== NO_OVERLAP) { // Draw sequence. var seq = orig_seq.slice(seq_offset, seq_offset + cig_len); // X center is offset + start - <half_sequence_length> @@ -2796,7 +2819,7 @@ if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) { // Draw sequence container. ctx.fillStyle = "yellow"; - ctx.fillRect(x_center, y_center - 9, s_end - s_start, 9); + ctx.fillRect(x_center - gap, y_center - 9, s_end - s_start, 9); draw_last[draw_last.length] = [x_center + (s_end - s_start)/2, y_center + 4, 5]; ctx.fillStyle = CONNECTOR_COLOR; // Based on overlap b/t sequence and tile, get sequence to be drawn. @@ -2817,15 +2840,15 @@ // Draw sequence. for (var c = 0, str_len = seq.length; c < str_len; c++) { var c_start = Math.floor( Math.max(0, (seq_start + c - tile_low) * w_scale) ); - ctx.fillText(seq[c], c_start + this.left_offset + gap - (s_end - s_start)/2, y_center); + ctx.fillText(seq[c], c_start + this.left_offset - (s_end - s_start)/2 - gap, y_center); } } else { // Draw block. ctx.fillStyle = "yellow"; // TODO: This is a pretty hack-ish way to fill rectangle based on mode. - ctx.fillRect(x_center, y_center + (this.mode != "Dense" ? 2 : 5), - s_end - s_start, (mode != "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT)); + ctx.fillRect(x_center, y_center + (this.mode !== "Dense" ? 2 : 5), + s_end - s_start, (mode !== "Dense" ? SQUISH_FEATURE_HEIGHT : DENSE_FEATURE_HEIGHT)); } } seq_offset += cig_len; @@ -2861,6 +2884,7 @@ y_center = (mode === "Dense" ? 1 : (1 + slot)) * y_scale, block_color = this.prefs.block_color, label_color = this.prefs.label_color; + gap = 0; // Left-gap for label text since we align chrom text to the position tick // Draw read. ctx.fillStyle = block_color; @@ -2893,12 +2917,15 @@ if (mode === "Pack" && feature_start > tile_low) { // Draw label. ctx.fillStyle = this.prefs.label_color; + if ( (mode === "Pack" || this.mode === "Auto") && w_scale > CHAR_WIDTH_PX) { + var gap = Math.round(w_scale/2); + } if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) { ctx.textAlign = "left"; - ctx.fillText(feature_name, f_end + left_offset + LABEL_SPACING, y_center + 8); + ctx.fillText(feature_name, f_end + left_offset + LABEL_SPACING - gap, y_center + 8); } else { ctx.textAlign = "right"; - ctx.fillText(feature_name, f_start + left_offset - LABEL_SPACING, y_center + 8); + ctx.fillText(feature_name, f_start + left_offset - LABEL_SPACING - gap, y_center + 8); } ctx.fillStyle = block_color; } @@ -2927,7 +2954,7 @@ // Postdraw init: once data has been fetched, reset data url, wait time and start indexing. var track = this; var post_init = function() { - if (track.data_cache.size() == 0) { + if (track.data_cache.size() === 0) { // Track still drawing initial data, so do nothing. setTimeout(post_init, 300); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Enable the ftype attribute for test outputs, fixes the sam-to-bam test.
by Bitbucket 01 Mar '11

01 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9e717f1746c8/ changeset: r5149:9e717f1746c8 user: natefoo date: 2011-03-01 21:46:35 summary: Enable the ftype attribute for test outputs, fixes the sam-to-bam test. affected #: 2 files (116 bytes) --- a/lib/galaxy/tools/__init__.py Tue Mar 01 15:21:25 2011 -0500 +++ b/lib/galaxy/tools/__init__.py Tue Mar 01 15:46:35 2011 -0500 @@ -642,6 +642,8 @@ attributes['delta'] = int( attrib.pop( 'delta', '10000' ) ) attributes['sort'] = util.string_as_bool( attrib.pop( 'sort', False ) ) attributes['extra_files'] = [] + if 'ftype' in attrib: + attributes['ftype'] = attrib['ftype'] for extra in output_elem.findall( 'extra_files' ): # File or directory, when directory, compare basename # by basename --- a/tools/samtools/sam_to_bam.xml Tue Mar 01 15:21:25 2011 -0500 +++ b/tools/samtools/sam_to_bam.xml Tue Mar 01 15:46:35 2011 -0500 @@ -60,7 +60,7 @@ --><param name="index_source" value="cached" /><param name="input1" value="3.sam" ftype="sam" dbkey="equCab2" /> - <output name="output1" file="sam_to_bam_out2.bam" /> + <output name="output1" file="sam_to_bam_out2.bam" ftype="bam" /></test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Update bwa_color_wrapper cached indices name to match the key used in the test data repository
by Bitbucket 01 Mar '11

01 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dd69759ef4a6/ changeset: r5148:dd69759ef4a6 user: natefoo date: 2011-03-01 21:21:25 summary: Update bwa_color_wrapper cached indices name to match the key used in the test data repository affected #: 1 file (6 bytes) --- a/tools/sr_mapping/bwa_color_wrapper.xml Tue Mar 01 13:00:27 2011 -0500 +++ b/tools/sr_mapping/bwa_color_wrapper.xml Tue Mar 01 15:21:25 2011 -0500 @@ -168,7 +168,7 @@ python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out5.u.sam bwa_wrapper_out5.sam --><param name="refGenomeSource" value="indexed" /> - <param name="indices" value="equCab2chrM_cs" /> + <param name="indices" value="equCab2chrM" /><param name="sPaired" value="paired" /><param name="input1" value="bwa_wrapper_in5.fastqcssanger" ftype="fastqcssanger" /><param name="input2" value="bwa_wrapper_in6.fastqcssanger" ftype="fastqcssanger" /> @@ -188,7 +188,7 @@ python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out6.u.sam bwa_wrapper_out6.sam --><param name="refGenomeSource" value="indexed" /> - <param name="indices" value="hg19chrX_midpart_cs" /> + <param name="indices" value="hg19chrX_midpart" /><param name="sPaired" value="single" /><param name="input1" value="bwa_wrapper_in4.fastqcssanger" ftype="fastqcssanger" /><param name="source_select" value="full" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Have YeastMine datasource tool point to the production server location and add configuration to tool_conf.xml.main.
by Bitbucket 01 Mar '11

01 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7a28ce53e034/ changeset: r5147:7a28ce53e034 user: dan date: 2011-03-01 19:00:27 summary: Have YeastMine datasource tool point to the production server location and add configuration to tool_conf.xml.main. affected #: 2 files (55 bytes) --- a/tool_conf.xml.main Mon Feb 28 15:17:35 2011 -0500 +++ b/tool_conf.xml.main Tue Mar 01 13:00:27 2011 -0500 @@ -11,6 +11,7 @@ <tool file="data_source/fly_modencode.xml" /><tool file="data_source/modmine.xml" /><tool file="data_source/ratmine.xml" /> + <tool file="data_source/yeastmine.xml" /><tool file="data_source/worm_modencode.xml" /><tool file="data_source/wormbase.xml" /><tool file="data_source/eupathdb.xml" /> --- a/tools/data_source/yeastmine.xml Mon Feb 28 15:17:35 2011 -0500 +++ b/tools/data_source/yeastmine.xml Tue Mar 01 13:00:27 2011 -0500 @@ -2,7 +2,7 @@ <tool name="YeastMine" id="yeastmine" tool_type="data_source"><description>server</description><command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://yeastmine-test.yeastgenome.org/yeastmine-dev/begin.do" check_values="false" method="get" target="_top"> + <inputs action="http://yeastmine.yeastgenome.org/yeastmine/begin.do" check_values="false" method="get" target="_top"><display>go to yeastMine server $GALAXY_URL</display></inputs><uihints minwidth="800"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Remove unused parameters from TopHat and Cufflinks tool tests.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/25a02a5c286f/ changeset: r5146:25a02a5c286f user: dan date: 2011-02-28 21:17:35 summary: Remove unused parameters from TopHat and Cufflinks tool tests. affected #: 2 files (171 bytes) --- a/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 15:03:45 2011 -0500 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon Feb 28 15:17:35 2011 -0500 @@ -105,7 +105,6 @@ <test><param name="sPaired" value="No"/><param name="input" value="cufflinks_in.sam"/> - <param name="mean_inner_distance" value="20"/><param name="max_intron_len" value="300000"/><param name="min_isoform_fraction" value="0.05"/><param name="pre_mrna_fraction" value="0.05"/> --- a/tools/ngs_rna/tophat_wrapper.xml Mon Feb 28 15:03:45 2011 -0500 +++ b/tools/ngs_rna/tophat_wrapper.xml Mon Feb 28 15:17:35 2011 -0500 @@ -448,7 +448,6 @@ <param name="splice_mismatches" value="0"/><param name="min_intron_length" value="70"/><param name="max_intron_length" value="500000"/> - <param name="quals_scale" value="default"/><param name="junction_filter" value="0.15"/><param name="max_multihits" value="40"/><param name="min_segment_intron" value="50" /> @@ -494,7 +493,6 @@ <param name="splice_mismatches" value="0"/><param name="min_intron_length" value="70"/><param name="max_intron_length" value="500000"/> - <param name="quals_scale" value="default"/><param name="junction_filter" value="0.15"/><param name="max_multihits" value="40"/><param name="min_segment_intron" value="50" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: rc: Adding tests for vcf extract and filter tools
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/162fb94f7621/ changeset: r5145:162fb94f7621 user: rc date: 2011-02-28 21:03:45 summary: Adding tests for vcf extract and filter tools affected #: 11 files (3.1 KB) Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: mosaik: Test case uses sim_size instead of diff now, to get around the changing RG tag.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/05b089557d0d/ changeset: r5144:05b089557d0d user: dannon date: 2011-02-28 20:32:36 summary: mosaik: Test case uses sim_size instead of diff now, to get around the changing RG tag. affected #: 1 file (18 bytes) --- a/tools/sr_mapping/mosaik.xml Mon Feb 28 14:04:53 2011 -0500 +++ b/tools/sr_mapping/mosaik.xml Mon Feb 28 14:32:36 2011 -0500 @@ -13,8 +13,7 @@ #end if MosaikBuild -fr #if $genomeSource.refGenomeSource == 'indexed': - ##$genomeSource.indexReference - ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] } + ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] } #else: $genomeSource.historyReference #end if @@ -95,7 +94,7 @@ <param name="act" value="35"/><param name="bw" value="19"/><param name="mhp" value="100"/> - <output name="output" ftype="sam" file="mosaik_test_out.sam" sort="True"/> + <output name="output" ftype="sam" file="mosaik_test_out.sam" compare="sim_size" delta="0"/></test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guru: Fixed functional test for 'compute q values' tool - q-value is rounded to 6 significant digits, which shouldn't differ between different runs of the tool.
by Bitbucket 28 Feb '11

28 Feb '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3dce98e473f1/ changeset: r5143:3dce98e473f1 user: guru date: 2011-02-28 20:04:53 summary: Fixed functional test for 'compute q values' tool - q-value is rounded to 6 significant digits, which shouldn't differ between different runs of the tool. Also, fixed a bug in microsatellite birth/death tool - cases where microsatellite boundaries aren't defined are skipped. affected #: 4 files (317 bytes) --- a/test-data/q_values.tabular Mon Feb 28 12:16:28 2011 -0500 +++ b/test-data/q_values.tabular Mon Feb 28 14:04:53 2011 -0500 @@ -1,4 +1,4 @@ -pi0: 0.243863648325601 +pi0: 0.243864 FDR level: 0.05 --- a/tools/regVariation/compute_q_values.pl Mon Feb 28 12:16:28 2011 -0500 +++ b/tools/regVariation/compute_q_values.pl Mon Feb 28 14:04:53 2011 -0500 @@ -11,6 +11,8 @@ use strict; use warnings; use IO::Handle; +use File::Temp qw/ tempfile tempdir /; +my $tdir = tempdir( CLEANUP => 0 ); # check to make sure having correct input and output files my $usage = "usage: compute_q_values.pl [TABULAR.in] [lambda] [pi0_method] [fdr_level] [robust] [TABULAR.out] [PDF.out] \n"; @@ -44,7 +46,8 @@ my $r_script; # R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values -# construct an R script file and save it in the same directory where the perl file is located +# construct an R script file and save it in a temp directory +chdir $tdir; $r_script = "q_values_computation.r"; open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; @@ -76,6 +79,7 @@ dev.off(); #save the q-values in the output file $q_valuesOutputFile + qobj\$pi0 <- signif(qobj\$pi0,digits=6) qwrite(qobj, filename=\"$q_valuesOutputFile\"); #options(show.error.messages = TRUE); --- a/tools/regVariation/compute_q_values.xml Mon Feb 28 12:16:28 2011 -0500 +++ b/tools/regVariation/compute_q_values.xml Mon Feb 28 14:04:53 2011 -0500 @@ -1,4 +1,4 @@ -<tool id="compute_q_values" name="Compute q-values" version="1.0.0"> +<tool id="compute_q_values" name="Compute q-values" version="1.0.1"><description>based on multiple simultaneous tests p-values</description><command interpreter="perl"> --- a/tools/regVariation/microsatellite_birthdeath.pl Mon Feb 28 12:16:28 2011 -0500 +++ b/tools/regVariation/microsatellite_birthdeath.pl Mon Feb 28 14:04:53 2011 -0500 @@ -643,7 +643,11 @@ my %microsatstarts=(); #1 WITHIN EACH ALIGNMENT, IF THERE EXISTS A MICROSATELLITE #2 THIS HASH CONTAINS THE START SITE OF THE MICROSATELLITE #3 WIHIN THE ALIGNMENT - + next if !defined $extreme_start; + next if !defined $extreme_end; + next if $extreme_start > length($sequences{$tags[0]}); + next if $extreme_start < 0; + next if $extreme_end > length($sequences{$tags[0]}); for my $i (0 ... $#tags){ #1 NOW THAT WE HAVE GATHERED INFORMATION REGARDING #2 SEQUENCE ALIGNMENT AND MICROSATELLITE COORDINATES @@ -3977,3 +3981,4 @@ foreach my $line (@_) {print "$line\n";} print "::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<\n"; } + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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